Okay let's see. The SharpDX.MediaFoundation files:
1. Make sure that you edit these files in the correct MonoGame version as well as project type. You might have edited the files in the UAP folder, not the UWP folder.
2. The .dll should be completely empty. Like you did.
3. The .xml should look like this: <?xml version="1.0"?> <0doc> <0/doc>. Sorry that the doc tags did not show last time, this forum automatically treats them as html elements and hides them, which I didn't realize. Make sure that you remove the 0s from the tags (couldn't get them to show otherwise).
Making sure that it did really work:
1. Navigate to the .appxupload directory.(C:......\Game\AppPackages)
2. Open or extract the .appxupload. I used 7zip.
3. Open or extract the .appxbundle.
4. Open or extract any of the .appx files. I extracted the x64.appx.
5. Search for SharpDX.MediaFoundation.dll, if it doesn't exist you have successfully bypassed the error. The packages that previously failed the certification should have the SharpDX.MediaFoundation.dll included.
The trick lies in making sure that you choose the correct MonoGame version as well as the correct project type.